Yes, it is. It can be rewarding but also can tedious. Even with an efficient storage system (labeled Akro Mills or similar brand containers for me), spending 20 minutes to find the parts, print the label, and pack it up all up for a small $3 order of a bunch of cheap, little parts is annoying. You can solve this with an order minimum, but I don't have one. The flip side is I do have an above mentioned s/h fee - I don't try to hide it, but not all buyers read terms. If your order consists of 1 .03 part from me you will pay a $1 fee, otherwise I'm losing money on fees and shipping materials, not to mention time. As a LEGO fan I like being able to ship buyers that 1 part they need, so I don't mind an order that nets me a total of 60 cents in the end after fees, shipping costs, etc.
My parts store is pretty small. I did buy some new sets when I first opened my BL to part out, but in hindsight I could eventually sell almost all of them on Amazon for more than I've made off of the parts with a lot less effort. Now I weigh the costs of completing a partial used set in a lot I pick up, and if its not worth the time / money to complete it, I part that out into the store - its the main source of additional parts for me. I think it depends on how large you want your store to be. If I wanted to grow significantly in parts, then I would seek out cost effective new sets for sure, but for now, its not worth it. The exception is the occasional damaged box set. Parts are just a plus factor for sets and Minifigures I make the most money off of in my store.
I know that there are some full time BL folks out there, I hope they are hear I would love to hear from them. I love LEGO but I can't imagine sorting it as my full time job!